|
| Status |
Public on Jul 07, 2020 |
| Title |
EZH2m+p+ zygote H3K27me2_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Zygotes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6 X PWK/PHJ
genotype: Ezh2m+/p+
tissue: Zygotes
chip antibody: H3K27me2 Active Motif; 61435)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were collected in Nuclei Extraction Buffer directly and sheared by micrococcal nuclease (MNase) at 25°C for 5 min. Then the samples were the was incubated with H3K27me2 antibody overnight with rotation under constant rotation on a rotator at 4°C. The next day, 10ul Dyna beads Protein A (Thermo Fisher Scientific) was added to each sample and incubated 2 hours up to overnight at 4 °C. Subsequently, the beads were washed twice with low salt wash buffer, twice high salt wash buffer. For each sample, 100 ul eluiton buffer were added to resuspend beads and incubated at 65℃ for 2h to elute DNA from the beads. The DNA was purified by phenol:chloroform:isoamyl alcohol method.
Then samples were subjected to ULI-NChIP library preparation. ULI-NChIP library was generated using the KAPA Hyper Prep Kit according to the manufacture’s protocol. Paired-end 150-bp sequencing was performed on a Illumina HiSeq 2500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The raw reads were processed by Trimmomatic (version 0.38) to cut adapters and to trim low quality reads with the minimal length 90bp and minimal quality of bases 20.
Clean reads were mapped to the mouse mm10 genome by Bowtie2 with parameters as described previously and the default parameters in zygote ChIP sequencing data.
High quality unique mapping was performed by Samtools with MAPQ more than 30 and self-coded Perl scripts.
The duplication reads were removed by Picard to obtain the non-redundant reads.
SNP split was utilized to split the maternal and paternal reads alignment with the allele-specific C57BL6 and PWK mm10 genome.
SICER was utilized to call peaks (windows 200, Gap 600, q value 1e-5) with SICER.sh module and the differential peaks were found with SICER-df.sh module
Genome_build: mm10
Supplementary_files_format_and_content: wig files of EZH2m+p+ and EZH2m-p+ zygotes H3K27me2 ChIP-seq. Genome1 represents maternal genome(C57BL/6J), and genome2 represents paternal genome(PWK). Depth.csv shows the result of H3K27me2 reads depth on each chromosome. The last four csv files shows annotated peaks called by SICER. bdg files were used to check the distribution of reads in the genome.
|
| |
|
| Submission date |
Jul 21, 2019 |
| Last update date |
Jul 07, 2020 |
| Contact name |
Qingyuan Sun |
| E-mail(s) |
sunqy@ioz.ac.cn
|
| Phone |
8601064807050
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Department |
State Key Laboratory of Stem Cell and Reproductive Biology
|
| Street address |
Beichen West Rd., Chaoyang
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE134592 |
The landscape of H3K27me2 in mice zygotes |
|
| Relations |
| BioSample |
SAMN12329000 |
| SRA |
SRX6479460 |
